octopi 1.4.0__py3-none-any.whl

octopi-1.4.0.dist-info/METADATA

@@ -0,0 +1,119 @@
+Metadata-Version: 2.4
+Name: octopi
+Version: 1.4.0
+Summary: Model architecture exploration for cryoET particle picking
+Project-URL: Homepage, https://github.com/chanzuckerberg/octopi
+Project-URL: Documentation, https://chanzuckerberg.github.io/octopi/
+Project-URL: Issues, https://github.com/chanzuckerberg/octopi/issues
+Author: Jonathan Schwartz, Kevin Zhao, Daniel Ji, Utz Ermel
+License: MIT
+License-File: LICENSE
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Classifier: Topic :: Scientific/Engineering :: Image Recognition
+Requires-Python: >=3.9
+Requires-Dist: copick
+Requires-Dist: copick-utils
+Requires-Dist: ipywidgets
+Requires-Dist: kaleido
+Requires-Dist: matplotlib
+Requires-Dist: mlflow
+Requires-Dist: monai
+Requires-Dist: mrcfile
+Requires-Dist: multiprocess
+Requires-Dist: nibabel
+Requires-Dist: optuna
+Requires-Dist: optuna-integration[botorch,pytorch-lightning]
+Requires-Dist: pandas
+Requires-Dist: python-dotenv
+Requires-Dist: requests
+Requires-Dist: rich-click
+Requires-Dist: torch-ema
+Requires-Dist: tqdm
+Provides-Extra: dev
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+Requires-Dist: pytest>=6.2.3; extra == 'dev'
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+Provides-Extra: docs
+Requires-Dist: mkdocs; extra == 'docs'
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+Requires-Dist: mkdocs-redirects; extra == 'docs'
+Description-Content-Type: text/markdown
+
+# OCTOPI 🐙🐙🐙
+
+[![License](https://img.shields.io/pypi/l/octopi.svg?color=green)](https://github.com/chanzuckerberg/octopi/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/octopi.svg?color=green)](https://pypi.org/project/octopi)
+[![Python Version](https://img.shields.io/pypi/pyversions/octopi.svg?color=green)](https://www.python.org/)
+
+**O**bject dete**CT**ion **O**f **P**rote**I**ns. A deep learning framework for Cryo-ET 3D particle picking with autonomous model exploration capabilities.
+
+## 🚀 Introduction
+
+octopi addresses a critical bottleneck in cryo-electron tomography (cryo-ET) research: the efficient identification and extraction of proteins within complex cellular environments. As advances in cryo-ET enable the collection of thousands of tomograms, the need for automated, accurate particle picking has become increasingly urgent.
+
+Our deep learning-based pipeline streamlines the training and execution of 3D autoencoder models specifically designed for cryo-ET particle picking. Built on [copick](https://github.com/copick/copick), a storage-agnostic API, octopi seamlessly accesses tomograms and segmentations across local and remote environments. 
+
+## 🧩 Core Features
+
+- **3D U-Net Training**: Train and evaluate custom 3D U-Net models for particle segmentation
+- **Automatic Architecture Search**: Explore optimal model configurations using Bayesian optimization via Optuna
+- **Flexible Data Access**: Seamlessly work with tomograms from local storage or remote data portals
+- **HPC Ready**: Built-in support for SLURM-based clusters
+- **Experiment Tracking**: Integrated MLflow support for monitoring training and optimization
+- **Dual Interface**: Use via command-line or Python API
+
+## 🚀 Quick Start
+
+### Installation
+
+Octopi is availableon PyPI and can be installed using pip:
+```bash
+pip install octopi
+```
+
+⚠️ **Note**: One of the current dependencies is currently not working with pip 25.1. We recommend using pip 25.2 or higher,
+or [`uv pip`](https://docs.astral.sh/uv/pip/) when installing octopi.
+```bash
+pip install --upgrade "pip>=25.2"
+```
+
+### Basic Usage
+
+octopi provides two main command-line interfaces:
+
+```bash
+# Main CLI for training, inference, and data processing
+octopi
+```
+
+## 📚 Documentation
+
+For detailed documentation, tutorials, CLI and API reference, visit our [documentation](https://chanzuckerberg.github.io/octopi/).
+
+## 🤝 Contributing
+
+## Code of Conduct
+
+This project adheres to the Contributor Covenant [code of conduct](https://github.com/chanzuckerberg/.github/blob/master/CODE_OF_CONDUCT.md).
+By participating, you are expected to uphold this code. 
+Please report unacceptable behavior to [opensource@chanzuckerberg.com](mailto:opensource@chanzuckerberg.com).
+
+## 🔒 Security
+
+If you believe you have found a security issue, please responsibly disclose by contacting us at security@chanzuckerberg.com.
+
+

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octopi-1.4.0.dist-info/WHEEL

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+Generator: hatchling 1.28.0
+Root-Is-Purelib: true
+Tag: py3-none-any

octopi-1.4.0.dist-info/entry_points.txt

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+[console_scripts]
+octopi = octopi.main:routines
+octopi-slurm = octopi.main:slurm_routines

octopi-1.4.0.dist-info/licenses/LICENSE

@@ -0,0 +1,41 @@
+# Legal
+
+## License for the octopi package
+
+This package is licensed under the MIT License:
+
+```
+MIT License
+
+Copyright (c) 2025 Chan Zuckerberg Initiative
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the "Software".
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE "SOFTWARE" OR THE USE OR OTHER DEALINGS IN THE
+"SOFTWARE".
+```
+
+## License Notice for Dependencies
+
+```
+This repository is licensed under the MIT License; however, it relies on certain third-party dependencies that are licensed under the GNU General Public License (GPL). Specifically:
+
+- monai is licensed under the Apache License 2.0.
+- pytorch-lightning is licensed under the Apache License 2.0.
+
+All dependencies use permissive open-source licenses that are compatible with this project's MIT License. No GPL or other copyleft licensed dependencies are included.
+For specific licensing information about any dependency, please refer to the respective package documentation or repository.
+```